Author Archives: ryanchisholm

Sam’s paper on modelling extinction debt published in Ecology Letters

When natural habitat is cleared, some species go extinct immediately, but others only after a period of time—the latter constitute an “extinction debt”. More habitat loss generally leads to greater species loss and greater extinction debt. But does the spatial pattern of habitat fragmentation matter? This issue is currently the topic of fervent debate in the ecological literature (see, e.g., here and here and here).

In a new Ecology Letters paper led by Sam Thompson, our recently graduated Imperial-NUS PhD student, we developed analytical methods for calculating extinction debt after habitat fragmentation in a spatial neutral model, i.e., a model that treats all species equally. Sam’s paper built on previous work by our lab looking at the immediate response of fragmentation to species richness, i.e., before extinction debt has been paid. Our new methods for estimating extinction debt in a neutral model are accurate and efficient to compute. They involve first calculating two key metrics, termed effective area and effective connectivity, and then plugging these into formulas.

Modelling approaches such as these are invaluable for understanding species loss with habitat fragmentation, because of the difficulty of carrying out large-scale habitat fragmentation experiments. One general insight from our analysis is that for a fragmentation metric to be biologically meaningful, it should be based on the way that the affected species interact with the landscape, rather than on what looks “fragmented” to the human eye.

Overall, we found that even in a neutral model the effect of habitat fragmentation on species loss is non-trivial and varies with spatial scale, temporal scale, and the degree of fragmentation. If this is true even in a neutral model, surely it must be true in reality. We suggest that this degree of subtlety is sometimes missing from the ongoing fragmentation debate, and that any discussion of fragmentation and species richness should be informed by rigorous modelling.

The paper was also coauthored by James Rosindell, Sam’s advisor at Imperial College London.

Thompson, S. E. D., R. A. Chisholm, and J. Rosindell (2019). Characterising extinction debt following habitat fragmentation using neutral theory. Ecology Letters (in press)


Trajectories of species loss following habitat clearing under different model scenarios for tropical forest trees corresponding to an area of ~5 km2. The shaded grey area to the right of each graph indicates extinction debt in every simulation, with light red and light blue areas additionally indicating the range of extinction debt across all simulations.

Population dynamics and species diversity workshop at Macquarie University

Ryan has just returned from a workshop on population dynamics and species diversity at Macquarie University, Sydney, Australia. The ten participants spent three days brainstorming new approaches to understanding how the dynamics of individual populations aggregate to determine properties of whole communities, including species diversity. As part of this, the participants spent time analysing a global dataset of community and population dynamics compiled from various sources by the workshop leaders, John Alroy and Drew Allen.

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Payal Dash completes her internship in the lab

Payal Dash recently completed a two-month internship in our lab. Payal is currently pursuing an Integrated Master’s degree at the National Institute of Science Education and Research in India. During her time in the lab, she worked to compile a database of feeding behaviours of the birds of Southeast Asia and spent time learning basic skills in theoretical ecology; in her spare time she visited some of Singapore’s nature-based attractions.


Visit by Kesara Anamthawat-Jónsson from the University of Iceland

Today the lab was visited by Prof. Kesara Anamhawat-Jónsson from the University of Iceland. Kesara delivered a fascinating talk about plant colonisation of the volcanic island of Surtsey, which lies about 20 km off the coast of the mainland of Iceland and was formed in a volcanic eruption in 1963. We also discussed Surtsey in the context of our lab’s work on island biogeography.


Chris attends the Hong Kong University International Conference of Undergraduate Research in Science

Chris Wei Ziyi is currently at the Hong Kong University International Conference of Undergraduate Research in Science. This conference brings together undergraduate researchers from around the world to share their ideas and meet professional scientists working at Hong Kong University. Chris presented a poster on his Honours thesis “Population modelling and projected control of invasive Javan Mynas in Singapore”, which led to stimulating discussions with fellow conference participants about urban bird invasions.

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Visit to Victoria University of Wellington

Ryan recently visited Victoria University of Wellington in New Zealand, where he met with researchers and delivered a seminar on our lab’s work on estimating rates of species extinctions. The seminar included both our work on historical Singapore extinctions and our work on extinctions due to fragmented habitat loss.


An aerial view of the University of Victoria campus (centre of image) with Wellington Harbour in the background. Image credit:

Sam has successfully defended his PhD thesis!

Sam successfully defended his PhD thesis this morning at Imperial College London in Silwood Park. Sam’s thesis deals with models of habitat fragmentation and species loss. Being jointly supervised by James Rosindell, of Imperial College, and Ryan, Sam has split his time over the past three and a half years between Imperial College and Singapore. Congratulations, Sam!


New paper on global patterns of nitrogen-fixing trees published in Journal of Ecology

Our new study, led by Duncan Menge, from Columbia University, and Tak, on global patterns of nitrogen-fixing tree abundance has just been published in Journal of Ecology. Symbiotic nitrogen-fixing (N-fixing) trees can supply large amounts of N to forests, and are important for ecosystem functioning. Patterns of abundance of N-fixing trees have been well studied in the Americas, but less well in other biogeographic regions.

In the new study, which included 82 co-authors from the CTFS-ForestGEO network, we examined patterns and drivers of N-fixing tree abundance in forests across different biogeographic regions. We used tree census data from 44 large CTFS-ForestGEO forest plots, comprising in total approximately 5,000 tree species and 4 million trees. Most of these plots were situated in America and Asia. In America, we confirmed the previously known pattern of a decrease in N-fixing tree abundance by an order of magnitude moving from the tropics towards the poles. In contrast, in Asia, we found no latitudinal gradient in N-fixing tree abundance; instead, abundance was uniformly low, and in particular N-fixing tree abundance in the Asian tropics was approximately six times lower than in the American tropics.

Our results suggest that recent estimates of N fixation rates used in global models may be too high, because they do not account for the Asian tropics having lower N-fixing tree abundance than the American tropics.

Duncan N. L. Menge, Ryan A. Chisholm, … and Tak Fung. Patterns of nitrogen-fixing tree abundance in forests across Asia and America. Journal of Ecology (in press)


Trees of the N-fixing species Andira inermis are found in three Panama CTFS-ForestGEO plots used in our study. Image credit: Wikipedia


Tak’s new paper on richness–productivity relationships in a neutral model published in Theoretical Ecology

The relationship between species richness and productivity has been extensively studied in ecology. However, despite decades of empirical and theoretical research, it remains unclear how the relationship changes with the spatial scale of observation. A new theoretical study led by Tak and published in Theoretical Ecology sheds some light on this question by showing how, even in a neutral model, increasing the spatial scale results in non-trivial changes to the richness–productivity relationship.

The study analyses a neutral model representing a local community of species populations competing for finite resources. We derived a mathematical formula for the richness–productivity relationship in this model. The resulting curve has a unimodal shape, consistent with previous simulation-based studies. The rising part of the relationship is driven by a sampling effect—more individuals typically comprise a greater number of species (the “more-individuals effect“). The declining part of the relationship is driven by a greater proportion of the pool of propagules being of local origin, which dilutes species diversity arising from immigrant propagules (the “dilution effect“).

Our study’s main novel finding is that the peak of the unimodal richness–productivity relationship from the model shifts to the left as spatial scale increases. The underlying reason is that an increase in spatial scale results in a greater area-to-perimeter ratio, which increases the strength of the dilution effect relative to that of the more-individuals effect. Thus, the increasing phase of the richness–productivity relationship is predicted to be more prominent on smaller spatial scales, while the decreasing phase is predicted to be more prominent on larger scales. These findings can potentially account for some of the observed scale-dependence of richness–productivity relationships in nature.

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Relationship between (expected) species richness and productivity from the model analysed, for a community with area 0.1 ha (left panel) and a community with area 1.6 ha (right panel). The peak of the unimodal relationship shifts to the left as the spatial scale increases. Image credit: CSIRO.

Fung, T., S. Xiao, R. A. Chisholm. Spatial scaling of species richness–productivity relationships for local communities: analytical results from a neutral model. Theoretical Ecology (in press)

UPDATE (June 2020): Tak’s paper has been recommended on Faculty Opinions (formerly F1000).